Do you have any error or warning message when did pdb2gmx? I think that there is an error during pdb2gmx. It may be because there is a nonstandard residue or missing parameter for ligand or non-amino acid. But, I am not sure unless know the error or warning message.

Initially, you do not have anything wrong, the topology looks like this because your protein has two different chains, and all of the topology parameters are in:

#include "topol_Protein_chain_A.itp"

#include "topol_Protein_chain_B.itp"

The newest version of Gromacs saves all the topology parameters in the .itp files instead of the topol.top if you have two chains, so It means that your protein has two N-terminal and two C-terminal if you do not expect that your protein has two chains, your .pdb file missed some residue. You can check it with some visualization programs such as VMD or Schrodinger. If you wish these two chains initially, you can continue with the methodology (assign cell, solvation, counterions, energy minimization, ...). Just consider that if you change the work folder, you should also copy the .itp files.

@Andres Cifuentes, thanks for the answer. pls, Which files (topol_proten_chain_A, topol_proten_chain_B or topol.top files) can i put these parameters ;

Include ligand topology

#include "LIG.itp", ;

Include ligand parameters

#include "LIG.prm"

THanks, I look forward for you response, Sir.

These parameters you must include in the topol.top file but there is a tricky part you should include .prm line after

; Include forcefield parameters

#include "./charmm36-feb2021.ff/forcefield.itp"

#include "LIG.prm"

and the ligand topology after water topology is good but the most important thing is the line after forcefield because the other way Gromacs is not going to recognize the ligand parameters. you can also check the gromacs tutorials on http://www.mdtutorials.com/gmx/

you can also obtain the parameters for the ligand (if you are using charmm force field) with swissparam https://www.swissparam.ch/